ViewVC Help
View Directory | Revision Log | Download Tarball | View Changeset | Root Listing
root/pdbwiki
Sticky Revision:
Sort logs by:
Revision 66 - Directory Listing
Modified Fri Sep 2 10:23:01 2011 UTC (4 years, 11 months ago) by jmduarteg
Fixed (this time hopefully for good) the beta character problem of entry 1ubp by hard-coding a fix in the python page generation script
Revision 65 - Directory Listing
Modified Fri Sep 2 07:56:59 2011 UTC (4 years, 11 months ago) by jmduarteg
Added hard-coded fix for a wrongly coded "beta" character in entry 1ubp also to update_structures.sh
Revision 64 - Directory Listing
Modified Thu Sep 1 15:08:14 2011 UTC (4 years, 11 months ago) by jmduarteg
Fixing hard-coded path of mmCIF gz directory 
Revision 63 - Directory Listing
Modified Thu Sep 1 15:02:10 2011 UTC (4 years, 11 months ago) by jmduarteg
Adapting the create_pdbentries.py script to read cif.gz files directly
Revision 62 - Directory Listing
Modified Thu Sep 1 13:54:20 2011 UTC (4 years, 11 months ago) by jmduarteg
Also updating the generate_more_images script with same changes as generate_images
Revision 61 - Directory Listing
Modified Thu Sep 1 13:50:52 2011 UTC (4 years, 11 months ago) by jmduarteg
Updating the generate image script to directly load pdb gzipped files
Revision 60 - Directory Listing
Modified Thu Sep 1 10:51:59 2011 UTC (4 years, 11 months ago) by jmduarteg
Made call to strptime compatible with python 2.4
Revision 59 - Directory Listing
Modified Thu Jul 28 12:50:59 2011 UTC (5 years, 1 month ago) by hstehr
adding our scripts to update the local pdb (via rsync)
Revision 58 - Directory Listing
Modified Thu Jul 28 10:40:41 2011 UTC (5 years, 1 month ago) by jmduarteg
Committing latest openmmsbatch jar with bug fix for deletion of entries
Revision 57 - Directory Listing
Modified Thu Jul 28 10:37:12 2011 UTC (5 years, 1 month ago) by jmduarteg
Fixed bug: deletions of entries was not working because the sql DELETE command was not being executed, no idea why the stmt.executeUpdate() call was missing
Revision 56 - Directory Listing
Modified Wed Jul 27 17:35:53 2011 UTC (5 years, 1 month ago) by jmduarteg
Now all parameters passed in the command line, nothing major hard-coded
Revision 55 - Directory Listing
Modified Wed Jul 27 17:22:11 2011 UTC (5 years, 1 month ago) by jmduarteg
Updated doc
Revision 54 - Directory Listing
Modified Wed Jul 27 16:52:57 2011 UTC (5 years, 1 month ago) by jmduarteg
Fixed a few issues with the scripts, now they should be usable from anywhere:
- the table names have to be uppercase (was working in molgen because mysql was in ignore case mode)
- db params were hard coded in a few places
- now using gz files directly instead of unzipped
Revision 53 - Directory Listing
Modified Wed Jul 27 16:42:10 2011 UTC (5 years, 1 month ago) by jmduarteg
Committing new openmmsbatch (used to be called openmms_new) with bugs fixed: now db params not hard coded, reading directly from zip works.
Revision 52 - Directory Listing
Modified Wed Jul 27 16:32:55 2011 UTC (5 years, 1 month ago) by jmduarteg
New stripped jar (without packages for which we have modified sources in src folder)
Removed the existing OpenMMS_new.jar, now it has to be generated from eclipse by checking out and generating executable jar
Revision 51 - Directory Listing
Modified Wed Jul 27 16:06:58 2011 UTC (5 years, 1 month ago) by jmduarteg
Committing two more packages extracted from the source jar and fixed bug in reading cif.gz file (bug was in class CifParser)
Revision 50 - Directory Listing
Modified Wed Jul 27 16:05:33 2011 UTC (5 years, 1 month ago) by jmduarteg
Fixed bug: db parameters were hard coded and not read from command line
Revision 49 - Directory Listing
Modified Wed Jul 27 14:18:44 2011 UTC (5 years, 1 month ago) by hstehr
added some script for data validation which I forgot to check in earlier
Revision 48 - Directory Listing
Modified Wed Jul 27 13:21:15 2011 UTC (5 years, 1 month ago) by jmduarteg
Adding the thre additional classes that the package contained in the original jar. That should help compilation and packaging.
Revision 47 - Directory Listing
Modified Wed Jul 27 13:00:15 2011 UTC (5 years, 1 month ago) by jmduarteg
Removing java files in old folder
Revision 46 - Directory Listing
Modified Wed Jul 27 12:57:49 2011 UTC (5 years, 1 month ago) by jmduarteg
Committing eclipse specific java project files. With this we should be able to check out into eclipse and have everything running out of the box
Revision 45 - Directory Listing
Modified Wed Jul 27 12:40:47 2011 UTC (5 years, 1 month ago) by jmduarteg
Adding src dir with full dirs matching java package names
Revision 44 - Directory Listing
Modified Wed Jul 27 08:59:06 2011 UTC (5 years, 1 month ago) by hstehr
adding pdbase update pipeline and modified openMMS package
Revision 43 - Directory Listing
Modified Tue Feb 1 12:34:29 2011 UTC (5 years, 6 months ago) by hstehr
Changed message for new QuestyCaptcha

Revision 42 - Directory Listing
Modified Tue Feb 1 11:34:17 2011 UTC (5 years, 6 months ago) by jmduarteg
Now works with ConfirmEdit extension. Probably does not work anymore with recaptcha, though in principle it could work with both as in theory ConfirmEdit also has ReCaptcha (but for some reason the package downloadable from the ConfirmEdit page does not contain ReCaptcha despite what they say in their docs)
Revision 41 - Directory Listing
Modified Mon Jan 3 15:12:40 2011 UTC (5 years, 7 months ago) by jmduarteg
Removing unused dependency SOAPpy
Revision 40 - Directory Listing
Modified Tue Dec 21 15:20:16 2010 UTC (5 years, 8 months ago) by jmduarteg
Another upper case
Revision 39 - Directory Listing
Modified Tue Dec 21 15:16:17 2010 UTC (5 years, 8 months ago) by jmduarteg
Changed table names to upper case to adapt to new db in bio.cc
Revision 38 - Directory Listing
Modified Tue Dec 21 14:54:03 2010 UTC (5 years, 8 months ago) by jmduarteg
Updated hard coded paths to new locations in bio.cc
Revision 37 - Directory Listing
Modified Tue Apr 13 10:05:16 2010 UTC (6 years, 4 months ago) by hstehr
adding some example code for generating biounit images
Revision 36 - Directory Listing
Modified Tue Mar 16 10:12:19 2010 UTC (6 years, 5 months ago) by hstehr
finally commiting alternative script for creating alternative images (qutemol-like, color by b-factor and others)
Revision 35 - Directory Listing
Modified Mon Mar 15 15:51:09 2010 UTC (6 years, 5 months ago) by jmduarteg
Getting rid of dependency of pyaglappe (just needed the three2oneletter and aas dictionaries)
Revision 34 - Directory Listing
Modified Fri Feb 19 15:49:06 2010 UTC (6 years, 6 months ago) by duarte
Made text box bigger. Added a comment about references.
Revision 33 - Directory Listing
Modified Fri Feb 12 13:42:43 2010 UTC (6 years, 6 months ago) by duarte
New feature: now a caption can be added. Parameters changed.
Revision 32 - Directory Listing
Modified Thu Feb 11 09:55:09 2010 UTC (6 years, 6 months ago) by duarte
protect structures 2jo7,3eqq,3en1 from being automatically deleted
Revision 31 - Directory Listing
Modified Thu Jul 30 11:46:24 2009 UTC (7 years, 1 month ago) by hstehr
changed message for successful submission of a comment (added info about how to edit/delete comments)
Revision 30 - Directory Listing
Modified Tue Jul 28 09:43:06 2009 UTC (7 years, 1 month ago) by duarte
Fixed bug: was using 'None' for some Unicode links when db contained a NULL, now making sure we don't select NULLs
Revision 29 - Directory Listing
Modified Sat Jun 27 10:13:33 2009 UTC (7 years, 2 months ago) by dmb
Put each extension into its own directory for easier management in the live extensions directory
Revision 28 - Directory Listing
Modified Thu Jun 25 13:11:42 2009 UTC (7 years, 2 months ago) by duarte
Implemented a cancel button, enabled in the main page but disabled in the Special "Process Article Comment" page.
Revision 27 - Directory Listing
Modified Thu Jun 25 08:27:18 2009 UTC (7 years, 2 months ago) by duarte
Fixed prefill of commenter name (was not being prefilled, but only added from login name)
Added link in captcha-failed message to original page.
Revision 26 - Directory Listing
Modified Wed Jun 24 15:43:56 2009 UTC (7 years, 2 months ago) by duarte
First implementation of captchas, thanks to Dan who got the code from Jim Wilson and Gunter!
Now options at level 1 are disabled in the category drop down and only options at level 2 or above are selectable.

Revision 25 - Directory Listing
Modified Mon May 25 13:11:30 2009 UTC (7 years, 3 months ago) by duarte
Tagging version 1.2. This is the pipeline we use for the pdbwiki 1.2 site.
Revision 24 - Directory Listing
Modified Fri May 15 15:23:42 2009 UTC (7 years, 3 months ago) by duarte
Removed obsolete file and updated a bit the procedure doc
Revision 23 - Directory Listing
Modified Fri May 15 13:19:14 2009 UTC (7 years, 3 months ago) by duarte
Changed 'add annotation' to 'add comment'
Revision 22 - Directory Listing
Modified Fri May 15 13:14:32 2009 UTC (7 years, 3 months ago) by duarte
Some modifications for clearer output
Revision 21 - Directory Listing
Modified Thu May 14 17:02:05 2009 UTC (7 years, 3 months ago) by duarte
Adapted scripts to redesign of comments system.
Fixed bug: the list of pic versions was not properly passed to upload_pages.sh and thus was not properly working, now using a comma separated list.
Revision 20 - Directory Listing
Modified Wed May 13 15:24:17 2009 UTC (7 years, 3 months ago) by duarte
Now adding automatically 'annotated entry' category
Removed the <div class='commentBlock'> markup
Now comments added above the {{PDB entry user comment footer}} text
Revision 19 - Directory Listing
Modified Fri May 8 13:28:23 2009 UTC (7 years, 3 months ago) by duarte
New update pipeline for version 1.2:
- using new listing scripts with last revision dates as timestamps. The delay offset for the timestamps not needed anymore: update now should work at any time of the week, it will always sync to current pdbase
- not deleting pages anymore in add/update/delete: now overwriting so that we keep the history in the wiki. No need to backup to xml files anymore
- deleted pages now contain link to "replaced by" structure
- now generating/deleting 3 images per entry

Revision 18 - Directory Listing
Modified Thu May 7 17:02:55 2009 UTC (7 years, 3 months ago) by duarte
New script to list non-empty user comment pages.
Revision 17 - Directory Listing
Modified Thu May 7 10:11:15 2009 UTC (7 years, 3 months ago) by duarte
Adapted to new lists with LAST_REVISION_DATEs. Got rid of DELAY offset, not needed anymore with the new system.
Revision 16 - Directory Listing
Modified Thu May 7 08:52:20 2009 UTC (7 years, 3 months ago) by duarte
Now getEntryList.php takes the LAST_REVISION_DATE of the entries by parsing the text of the latest version of the page.
New script getLastRevDatesPdbase.sh to get the last revision dates of all entries from pdbase.
Revision 15 - Directory Listing
Modified Thu May 7 08:41:42 2009 UTC (7 years, 3 months ago) by duarte
Now getting the latest revision date instead of creation date. Committing just to keep the code for the record, we never really used this version.
Revision 14 - Directory Listing
Modified Tue May 5 09:50:27 2009 UTC (7 years, 3 months ago) by duarte
Changed pics dir to new_pics. Changed minimum required count of entries from wiki to 50000
Revision 13 - Directory Listing
Modified Tue May 5 09:03:28 2009 UTC (7 years, 3 months ago) by duarte
Fixed bug: had forgotten to remove a replacement string after getting rid of hard links to comments.
Revision 12 - Directory Listing
Modified Tue May 5 08:14:05 2009 UTC (7 years, 3 months ago) by duarte
Got rid of hard link to user comments template. Now using the comments extension instead.
Revision 11 - Directory Listing
Modified Mon May 4 10:21:58 2009 UTC (7 years, 3 months ago) by hstehr
updated image generation (spheres+cartoon+thumbs), new distributed rendering script

Revision 10 - Directory Listing
Modified Sun May 3 19:04:57 2009 UTC (7 years, 3 months ago) by jmduarteg
Now categories come from a static list instead of dynamically querying the database. This is a temporary fix while we don't find a faster way of querying.
Revision 9 - Directory Listing
Modified Wed Apr 8 15:53:25 2009 UTC (7 years, 4 months ago) by duarte
Got rid of redirection in comment.
Now lines starting with "#" will be ignored in the list file.
Revision 8 - Directory Listing
Modified Tue Mar 17 13:56:06 2009 UTC (7 years, 5 months ago) by duarte
Now purging the article page, solving an annoying bug.
Revision 7 - Directory Listing
Modified Fri Mar 13 16:53:07 2009 UTC (7 years, 5 months ago) by duarte
New title field that's, now the title is the header of the comment (level 3 header now). Changed the text of some tags, including in the submission confirmation page.
Revision 6 - Directory Listing
Modified Fri Mar 13 09:59:52 2009 UTC (7 years, 5 months ago) by duarte
Now comments can go to the User comments template instead of the Talk page.
Revision 5 - Directory Listing
Modified Wed Mar 11 19:10:50 2009 UTC (7 years, 5 months ago) by duarte
Now stripping spaces and adding Category: prefix using proper MediaWiki calls (instead of hacking it myself)
Revision 4 - Directory Listing
Modified Wed Mar 11 16:00:05 2009 UTC (7 years, 5 months ago) by duarte
Got rid of default root category. Now the $wgArticleCommentDefaults['rootCatComments'] setting acts as a switch (if not set no category drop-down is shown)
Revision 3 - Directory Listing
Modified Wed Mar 11 12:05:07 2009 UTC (7 years, 5 months ago) by duarte
First version of PDBWiki specific modification: now comments form includes a drop down of categories to be added with the comment.
Revision 2 - Directory Listing
Modified Wed Mar 11 12:03:44 2009 UTC (7 years, 5 months ago) by duarte
Initial commit of the ArticleComments.php. This is the original extension from the author. We'll be modifying next revisions.
Revision 1 - Directory Listing
Added Wed Mar 4 22:43:29 2009 UTC (7 years, 5 months ago) by jmduarteg
Initial commit to bioinformatics.org